You just suck at it. Think about projectory and physics. You obviously don't shoot at the towers when the cannon highlighted path is RIGHT on the towers. Your ship is moving therefore you have shoot a little beforehand. Also upgrade your ship. It's on the table right next to the old guy that you talk to to see the missions. Get another cannon or incendiary cannon fire and you can buy things that fortify damage soak of your ship. Also you can essentially go out as far as you can on that mission to where the mortars can't even reach and come back around. Also covering pretty much makes you take zero damage once you have no more damage left to spare.